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#3701 Response to stimulus
closed-out-of-date
5
2011-07-13
2006-11-23
No
Hello GO team,
We are having difficulty determining to which functional classes of proteins should curation of terms within the biological process hierarchy of "response to stimulus" (GO term #50896) be applied. The GO definition for response to stimulus (and similarly for many response to XXX terms) is, “ A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a specified stimulus.”
This definition seems to imply that a wide array of proteins, including receptors, intracellular proteins directly bound to the receptor, subsequent downstream signaling molecules, transcription factors and the genes that they regulate may all be considered as part of a response to a stimulus.
We desire clarification on this point, whether all these classes of proteins may be considered for curation of terms within the response to stimulus hierarchy, or should curation within this hierarchy be limited to only certain classes of proteins?
Thanks and Regards,
Jesintha.
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we think this will fall into place when we solve the protein stimulus question in SF 1601557
The scope of response_to was discussed at the Geneva annotation camp last summer. The outcome is documented here:
http://gocwiki.geneontology.org/index.php/Guidelines_from_Annotation_Camp#.27Response_to.27_guidelines
In summary, the definitions of the response to terms were updated to include a start and end point. 'Any process that results in a change....The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
(see GO:0050896)
The response to terms are very broad and include both the signaling pathway and the cellular process downstream of the signaling pathway (generally transcription).
We have therefore been making the signaling pathways children of the 'response to' terms, where appropriate.
There is a topic on the GO signaling wiki of how 'response to' and 'signaling' terms are related:
http://gocwiki.geneontology.org/index.php/Response_to_and_signaling
Please note that the top level 'response to' terms should not be used for direct annotation. A more specific term should be used instead.
I'll close this SF item, but it will be archived for reference.
Thanks
Becky